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<a href="code_structure_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/**</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment"> * @page codestructure Code Structure</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment"> *</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment"> * The code is divided into three parts: the (optional) parameters file, user defined functions, and core functions.</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment"> * The parameters file includes the definition of parameters used in the simulation (mesh refinement, time step size, material parameters, etc.).</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment"> * The user defined functions is a list of functions that can/must be defined by the user.</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment"> * The \c defineParameters and \c residual functions (italicized) require a user definition;</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment"> * the remaining functions have default definitions that can be overridden by the user if desired.</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment"> * These user functions are called by the core functions, as shown in the following diagram.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment"> *</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment"> * @dot</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment"> digraph G</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">{</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">  graph[rankdir=&quot;LR&quot;,bgcolor=&quot;transparent&quot;,splines=&quot;ortho&quot;];</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment"></span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">  Subgraph cluster_parametersFile{</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">   node [fontname=&quot;FreeSans&quot;,fontsize=13,fontcolor=&quot;black&quot;,</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">        shape=record,height=0.2,width=0.4,</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">        color=&quot;black&quot;, fillcolor=&quot;white&quot;, style=&quot;filled&quot;];</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">   fontname=&quot;FreeSans&quot;;</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">   fontsize=15;</span></div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">   label=&lt;&lt;U&gt;  Level 2 users &lt;/U&gt;&lt;BR/&gt; &lt;BR/&gt;Parameters file&gt;;</span></div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="comment">   color=&quot;transparent&quot;;</span></div>
<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;<span class="comment">   space1 [color=&quot;transparent&quot;,label=&quot;&quot;];</span></div>
<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;<span class="comment">   space2 [color=&quot;transparent&quot;,label=&quot;&quot;];</span></div>
<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;<span class="comment">   params [label=&quot;parameters.prm&quot;];</span></div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<span class="comment">   space3 [color=&quot;transparent&quot;,label=&quot;&quot;];</span></div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;<span class="comment">   space4 [color=&quot;transparent&quot;,label=&quot;&quot;];</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">   space5 [color=&quot;transparent&quot;,label=&quot;&quot;];</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">   space6 [color=&quot;transparent&quot;,label=&quot;&quot;];</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">   space7 [color=&quot;transparent&quot;,label=&quot;&quot;];</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">   {rank=same; space1, space2, params, space3, space4, space5, space6, space7}</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">  }</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;<span class="comment"></span></div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="comment">  Subgraph cluster_userFunctions{</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="comment">   node [fontname=&quot;FreeSans&quot;,fontsize=13,fontcolor=&quot;blue&quot;,</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="comment">        shape=record,height=0.2,width=0.4,</span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="comment">        color=&quot;black&quot;, fillcolor=&quot;white&quot;, style=&quot;filled&quot;];</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="comment">   fontname=&quot;FreeSans&quot;;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="comment">   fontsize=15;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="comment">   label=&lt;&lt;U&gt;  Level 1 users &lt;/U&gt;&lt;BR/&gt; &lt;BR/&gt;User defined functions&gt;;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="comment">   color=&quot;transparent&quot;;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="comment">   scalarIC [label=&quot;scalarInitialConditions&quot;,URL=&quot;\ref scalarInitialConditions&quot;];</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="comment">   vectorIC [label=&quot;vectorInitialConditions&quot;,URL=&quot;\ref vectorInitialConditions&quot;];</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="comment">   defineParameters [label=&lt;{&lt;B&gt;&lt;I&gt;defineParameters&lt;/I&gt;&lt;/B&gt;}&gt;,URL=&quot;\ref defineParameters&quot;];</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="comment">   BCs [label=&quot;boundaryConditions&quot;,URL=&quot;\ref boundaryConditions&quot;];</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="comment">   residual [label=&lt;{&lt;B&gt;&lt;I&gt;residual&lt;/I&gt;&lt;/B&gt;}&gt;,URL=&quot;\ref residual&quot;];</span></div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;<span class="comment">   loadStep [label=&quot;loadStep&quot;,URL=&quot;\ref loadStep&quot;];</span></div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;<span class="comment">   adaptiveTS [label=&quot;adaptiveTimeStep&quot;,URL=&quot;\ref adaptiveTimeStep&quot;];</span></div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;<span class="comment">   projectFields [label=&quot;projectFields&quot;,URL=&quot;\ref projectFields&quot;];</span></div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;<span class="comment">   {rank=same; scalarIC, vectorIC, BCs, loadStep, adaptiveTS, residual, defineParameters, projectFields}</span></div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;<span class="comment">  }</span></div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;<span class="comment"></span></div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;<span class="comment">  subgraph cluster_baseFunctions{</span></div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;<span class="comment">   node [fontname=&quot;FreeSans&quot;,fontsize=13,fontcolor=&quot;blue&quot;,</span></div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;<span class="comment">        shape=record,height=0.2,width=0.4,</span></div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;<span class="comment">        color=&quot;black&quot;, fillcolor=&quot;white&quot;, style=&quot;filled&quot;];</span></div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;<span class="comment">   fontname=&quot;FreeSans&quot;;</span></div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;<span class="comment">   fontsize=15;</span></div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;<span class="comment">   label = &lt;&lt;u&gt;  Developer level  &lt;/u&gt;&lt;br/&gt; &lt;br/&gt;Core functions&gt;;</span></div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;<span class="comment">   color=&quot;transparent&quot;;</span></div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;<span class="comment">   Space1 [color=&quot;transparent&quot;,label=&quot;&quot;];</span></div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;<span class="comment">   formIC [label=&quot;FormInitialCondition&quot;,URL=&quot;\ref FormInitialCondition&quot;];</span></div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;<span class="comment">   setup [label=&quot;Setup&quot;,URL=&quot;\ref Setup&quot;];</span></div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;<span class="comment">   Space2 [color=&quot;transparent&quot;,label=&quot;&quot;];</span></div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;<span class="comment">   quadPtResidual [label=&quot;QuadPtResidual&quot;,URL=&quot;\ref QuadPtResidual&quot;];</span></div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;<span class="comment">   StepUpdate [label=&quot;StepUpdate&quot;,URL=&quot;\ref StepUpdate&quot;];</span></div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;<span class="comment">   Space3 [color=&quot;transparent&quot;,label=&quot;&quot;];</span></div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;<span class="comment">   ProjectionResidual [label=&quot;ProjectionResidual&quot;,URL=&quot;\ref ProjectionResidual&quot;];</span></div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;<span class="comment">   {rank=same; Space1, formIC, setup, Space2, quadPtResidual, StepUpdate, Space3, ProjectionResidual}</span></div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;<span class="comment">  }</span></div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;<span class="comment"></span></div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;<span class="comment">  subgraph cluster_worflow{</span></div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;<span class="comment">   node [fontname=&quot;FreeSans&quot;,fontsize=13,</span></div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;<span class="comment">        color=&quot;black&quot;, fillcolor=&quot;white&quot;, style=&quot;filled&quot;];</span></div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;<span class="comment">   fontname=&quot;FreeSans&quot;;</span></div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;<span class="comment">   fontsize=15;</span></div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;<span class="comment">   label = &lt;Workflow&lt;br/&gt;&lt;font color=&quot;white&quot;&gt;.&lt;/font&gt; &gt;;</span></div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;<span class="comment">   color=&quot;transparent&quot;;</span></div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;<span class="comment">   SETUP [label=&quot;\nSETUP\n\n&quot;];</span></div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;<span class="comment">   ASSMBLY [label=&quot;\nASSEMBLY\n\n&quot;];</span></div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;<span class="comment">   SOLVE [label=&quot;\nSOLVE\n\n&quot;];</span></div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;<span class="comment">   PP [label=&quot;\nPOSTPROCESSING\n\n&quot;];</span></div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;<span class="comment">   {rank=same; SETUP, ASSMBLY, SOLVE, PP}</span></div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;<span class="comment">  }</span></div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;<span class="comment"></span></div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;<span class="comment">  d1 [shape=point,width=0.001,height=0.001];</span></div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;<span class="comment">  d2 [shape=point,width=0.001,height=0.001];</span></div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;<span class="comment">  d3 [shape=point,width=0.001,height=0.001];</span></div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;<span class="comment"></span></div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;<span class="comment">  params -&gt; defineParameters [color=&quot;black&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;];</span></div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;<span class="comment">  {scalarIC,vectorIC} -&gt; d1 [color=&quot;black&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;,dir=none];</span></div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;<span class="comment">  d1 -&gt; formIC [color=&quot;black&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;];</span></div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;<span class="comment">  formIC -&gt; setup [color=&quot;black&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;];</span></div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;<span class="comment">  {defineParameters,BCs} -&gt; d2 [color=&quot;black&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;,dir=none];</span></div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;<span class="comment">  d2 -&gt; setup [color=&quot;black&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;];</span></div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;<span class="comment">  residual -&gt; quadPtResidual [color=&quot;black&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;];</span></div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;<span class="comment">  {loadStep,adaptiveTS} -&gt; d3 [color=&quot;black&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;,dir=none];</span></div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;<span class="comment">  d3 -&gt; StepUpdate [color=&quot;black&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;];</span></div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;<span class="comment">  projectFields -&gt; ProjectionResidual [color=&quot;black&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;];</span></div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;<span class="comment">  formIC -&gt; SETUP [color=&quot;transparent&quot;,fontsize=10,style=&quot;dashed&quot;,arrowhead=&quot;none&quot;,fontname=&quot;FreeSans&quot;];</span></div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;<span class="comment">  quadPtResidual -&gt; ASSMBLY [color=&quot;transparent&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;];</span></div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;<span class="comment">  StepUpdate -&gt; SOLVE [color=&quot;transparent&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;];</span></div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;<span class="comment">  ProjectionResidual -&gt; PP [color=&quot;transparent&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;];</span></div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;<span class="comment">  SETUP -&gt; ASSMBLY [color=&quot;black&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;,dir=none];</span></div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;<span class="comment">  ASSMBLY -&gt; SOLVE [color=&quot;black&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;,dir=none];</span></div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;<span class="comment">  SOLVE -&gt; PP [color=&quot;black&quot;,fontsize=10,style=&quot;solid&quot;,fontname=&quot;FreeSans&quot;,dir=none];</span></div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;<span class="comment">}</span></div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;<span class="comment"> * @enddot</span></div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;<span class="comment"> *</span></div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;<span class="comment"> */</span></div>
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